Variant report

Variant	rs12330584
Chromosome Location	chr3:180011968-180011969
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:180011263..180013073-chr3:180015745..180018246,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs13315674	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13327834	1.00[AMR][1000 genomes]
rs13327863	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28447629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28733407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28840838	1.00[AMR][1000 genomes]
rs28896899	1.00[AMR][1000 genomes]
rs73063365	1.00[AMR][1000 genomes]
rs73063390	1.00[AMR][1000 genomes]
rs73065365	1.00[AMR][1000 genomes]
rs73065371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73065372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73065386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9818857	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9823915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9829030	1.00[ASW][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9829787	1.00[AMR][1000 genomes]
rs9831310	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9833897	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9839988	1.00[AFR][1000 genomes]
rs9840843	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9851756	1.00[AMR][1000 genomes]
rs9852598	1.00[AMR][1000 genomes]
rs9856578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9864360	1.00[AMR][1000 genomes]
rs9865880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9869708	1.00[AMR][1000 genomes]
rs9871424	1.00[AMR][1000 genomes]
rs9878327	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9879382	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9883933	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012271	chr3:179806875-180234871	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv878040	chr3:179823887-180128288	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv997388	chr3:179899279-180172349	Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv536817	chr3:179899279-180172349	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv878041	chr3:179983857-180097855	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:180002800-180013600	Weak transcription	HMEC	breast
2	chr3:180003400-180013600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:180011600-180012400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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